Wednesday, 30 November 2011

[Bio-bwa-help] BWA unique mapping, multireads

removing BWA multiple mapped reads 

Notes (credit Li Heng) 

For single-end mapping, you can use X0:i:1 and/or XT:A:U. tags to filter

But for paired-end mapping, reads may be moved in the process of pairing. 
Most of those X? tags are computed for single-end mapping. That is also why some X? tags are missing in "sampe".

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